CRAN Package Check Results for Package NSA

Last updated on 2019-01-26 15:47:41 CET.

Check Details

Version: 0.0.32
Check: package dependencies
Result: NOTE
    Depends: includes the non-default packages:
     'R.methodsS3', 'MASS', 'matrixStats', 'R.oo', 'R.utils',
     'aroma.core', 'aroma.affymetrix', 'DNAcopy'
    Adding so many packages to the search path is excessive and importing
    selectively is preferable.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64

Version: 0.0.32
Check: top-level files
Result: NOTE
    Non-standard file/directory found at top level:
     ‘incl’
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 0.0.32
Check: dependencies in R code
Result: NOTE
    Packages in Depends field not imported from:
     ‘DNAcopy’ ‘MASS’ ‘R.methodsS3’ ‘R.oo’ ‘aroma.affymetrix’ ‘aroma.core’
     ‘matrixStats’
     These packages need to be imported from (in the NAMESPACE file)
     for when this namespace is loaded but not attached.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.0.32
Check: S3 generic/method consistency
Result: NOTE
    Found the following apparent S3 methods exported but not registered:
     NSAByTotalAndFracB.matrix allocateOutputDataSets.NSANormalization
     allocateOutputDataSets.SNPsNormalization
     allocateOutputDataSets.SampleNormalization
     as.character.NSANormalization as.character.SNPsNormalization
     as.character.SampleNormalization findArraysTodo.NSANormalization
     findArraysTodo.SampleNormalization findUnitsTodo.SNPsNormalization
     fitNSA.matrix fitNSAcnPs.matrix getDataSets.NSANormalization
     getDataSets.SNPsNormalization getDataSets.SampleNormalization
     getName.NSANormalization getName.SNPsNormalization
     getName.SampleNormalization getOutputDataSets.NSANormalization
     getOutputDataSets.SNPsNormalization
     getOutputDataSets.SampleNormalization getPath.NSANormalization
     getPath.SNPsNormalization getPath.SampleNormalization
     getRootPath.NSANormalization getRootPath.SNPsNormalization
     getRootPath.SampleNormalization process.NSANormalization
     process.SNPsNormalization process.SampleNormalization
     sampleNByTotalAndFracB.numeric snpsNByTotalAndFracB.matrix
    See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
    manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64

Version: 0.0.32
Check: R code for possible problems
Result: NOTE
    NB: .First.lib is obsolete and will not be used in R >= 3.0.0
    
    .First.lib: no visible global function definition for
     ‘packageDescription’
    NSAByTotalAndFracB.matrix: no visible global function definition for
     ‘throw’
    NSAByTotalAndFracB.matrix: no visible global function definition for
     ‘str’
    NSANormalization: no visible global function definition for ‘throw’
    NSANormalization: no visible global function definition for
     ‘getChipType’
    NSANormalization: no visible global function definition for
     ‘nbrOfFiles’
    NSANormalization: no visible global function definition for ‘getNames’
    NSANormalization: no visible global function definition for ‘extend’
    NSANormalization: no visible global function definition for ‘Object’
    NSANormalization: no visible global function definition for ‘setTags’
    SNPsNormalization: no visible global function definition for ‘throw’
    SNPsNormalization: no visible global function definition for
     ‘getChipType’
    SNPsNormalization: no visible global function definition for ‘getNames’
    SNPsNormalization: no visible global function definition for ‘extend’
    SNPsNormalization: no visible global function definition for ‘Object’
    SNPsNormalization: no visible global function definition for ‘setTags’
    SampleNormalization: no visible global function definition for ‘throw’
    SampleNormalization: no visible global function definition for
     ‘getChipType’
    SampleNormalization: no visible global function definition for
     ‘nbrOfFiles’
    SampleNormalization: no visible global function definition for
     ‘getNames’
    SampleNormalization: no visible global function definition for ‘extend’
    SampleNormalization: no visible global function definition for ‘Object’
    SampleNormalization: no visible global function definition for
     ‘setTags’
    allocateOutputDataSets.NSANormalization: no visible global function
     definition for ‘getPath’
    allocateOutputDataSets.NSANormalization: no visible global function
     definition for ‘getName’
    allocateOutputDataSets.NSANormalization: no visible global function
     definition for ‘getFile’
    allocateOutputDataSets.NSANormalization: no visible global function
     definition for ‘getPathname’
    allocateOutputDataSets.NSANormalization: no visible global function
     definition for ‘newInstance’
    allocateOutputDataSets.NSANormalization: no visible global function
     definition for ‘throw’
    allocateOutputDataSets.NSANormalization: no visible global function
     definition for ‘byPath’
    allocateOutputDataSets.SNPsNormalization: no visible global function
     definition for ‘getPath’
    allocateOutputDataSets.SNPsNormalization: no visible global function
     definition for ‘getName’
    allocateOutputDataSets.SNPsNormalization: no visible global function
     definition for ‘getFile’
    allocateOutputDataSets.SNPsNormalization: no visible global function
     definition for ‘nbrOfFiles’
    allocateOutputDataSets.SNPsNormalization: no visible global function
     definition for ‘getPathname’
    allocateOutputDataSets.SNPsNormalization: no visible global function
     definition for ‘newInstance’
    allocateOutputDataSets.SNPsNormalization: no visible global function
     definition for ‘throw’
    allocateOutputDataSets.SNPsNormalization: no visible global function
     definition for ‘byPath’
    allocateOutputDataSets.SNPsNormalization: no visible global function
     definition for ‘getPathnames’
    allocateOutputDataSets.SampleNormalization: no visible global function
     definition for ‘getPath’
    allocateOutputDataSets.SampleNormalization: no visible global function
     definition for ‘getName’
    allocateOutputDataSets.SampleNormalization: no visible global function
     definition for ‘getFile’
    allocateOutputDataSets.SampleNormalization: no visible global function
     definition for ‘nbrOfFiles’
    allocateOutputDataSets.SampleNormalization: no visible global function
     definition for ‘getPathname’
    allocateOutputDataSets.SampleNormalization: no visible global function
     definition for ‘newInstance’
    allocateOutputDataSets.SampleNormalization: no visible global function
     definition for ‘throw’
    allocateOutputDataSets.SampleNormalization: no visible global function
     definition for ‘byPath’
    allocateOutputDataSets.SampleNormalization: no visible global function
     definition for ‘getPathnames’
    findArraysTodo.NSANormalization: no visible global function definition
     for ‘getNames’
    findArraysTodo.NSANormalization: no visible global function definition
     for ‘getChipType’
    findArraysTodo.NSANormalization: no visible binding for global variable
     ‘AffymetrixCdfFile’
    findArraysTodo.NSANormalization: no visible global function definition
     for ‘getGenomeInformation’
    findArraysTodo.NSANormalization: no visible global function definition
     for ‘getUnitsOnChromosome’
    findArraysTodo.NSANormalization: no visible global function definition
     for ‘getFile’
    findArraysTodo.NSANormalization: no visible global function definition
     for ‘getName’
    findArraysTodo.NSANormalization: no visible global function definition
     for ‘str’
    findArraysTodo.SampleNormalization: no visible global function
     definition for ‘getNames’
    findArraysTodo.SampleNormalization: no visible global function
     definition for ‘getChipType’
    findArraysTodo.SampleNormalization: no visible binding for global
     variable ‘AffymetrixCdfFile’
    findArraysTodo.SampleNormalization: no visible global function
     definition for ‘getGenomeInformation’
    findArraysTodo.SampleNormalization: no visible global function
     definition for ‘getUnitsOnChromosome’
    findArraysTodo.SampleNormalization: no visible global function
     definition for ‘getFile’
    findArraysTodo.SampleNormalization: no visible global function
     definition for ‘getName’
    findArraysTodo.SampleNormalization: no visible global function
     definition for ‘str’
    findUnitsTodo.SNPsNormalization: no visible global function definition
     for ‘getFullNames’
    findUnitsTodo.SNPsNormalization: no visible global function definition
     for ‘str’
    findUnitsTodo.SNPsNormalization: no visible global function definition
     for ‘getFile’
    fitNSA.matrix: no visible binding for global variable ‘verbose’
    fitNSAcnPs.matrix: no visible global function definition for
     ‘approxfun’
    fitOneNSA: no visible global function definition for ‘hist’
    fitOneNSA: no visible global function definition for ‘CNA’
    fitOneNSA: no visible global function definition for ‘segment’
    fitSNPsN: no visible global function definition for ‘rowMedians’
    fitSample: no visible global function definition for ‘median’
    getFullName.NSANormalization: no visible global function definition for
     ‘getName’
    getFullName.NSANormalization: no visible global function definition for
     ‘getTags’
    getFullName.SNPsNormalization: no visible global function definition
     for ‘getName’
    getFullName.SNPsNormalization: no visible global function definition
     for ‘getTags’
    getFullName.SampleNormalization: no visible global function definition
     for ‘getName’
    getFullName.SampleNormalization: no visible global function definition
     for ‘getTags’
    getName.NSANormalization: no visible global function definition for
     ‘getName’
    getName.SNPsNormalization: no visible global function definition for
     ‘getName’
    getName.SampleNormalization: no visible global function definition for
     ‘getName’
    getPath.NSANormalization: no visible global function definition for
     ‘getRootPath’
    getPath.NSANormalization: no visible global function definition for
     ‘getFullName’
    getPath.NSANormalization: no visible global function definition for
     ‘getChipType’
    getPath.NSANormalization: no visible global function definition for
     ‘getPath’
    getPath.NSANormalization: no visible global function definition for
     ‘throw’
    getPath.SNPsNormalization: no visible global function definition for
     ‘getRootPath’
    getPath.SNPsNormalization: no visible global function definition for
     ‘getFullName’
    getPath.SNPsNormalization: no visible global function definition for
     ‘getChipType’
    getPath.SNPsNormalization: no visible global function definition for
     ‘getPath’
    getPath.SNPsNormalization: no visible global function definition for
     ‘throw’
    getPath.SampleNormalization: no visible global function definition for
     ‘getRootPath’
    getPath.SampleNormalization: no visible global function definition for
     ‘getFullName’
    getPath.SampleNormalization: no visible global function definition for
     ‘getChipType’
    getPath.SampleNormalization: no visible global function definition for
     ‘getPath’
    getPath.SampleNormalization: no visible global function definition for
     ‘throw’
    getTags.NSANormalization: no visible global function definition for
     ‘getTags’
    getTags.NSANormalization: no visible global function definition for
     ‘getAsteriskTags’
    getTags.SNPsNormalization: no visible global function definition for
     ‘getTags’
    getTags.SNPsNormalization: no visible global function definition for
     ‘getAsteriskTags’
    getTags.SampleNormalization: no visible global function definition for
     ‘getTags’
    getTags.SampleNormalization: no visible global function definition for
     ‘getAsteriskTags’
    nbrOfFiles.NSANormalization: no visible global function definition for
     ‘nbrOfFiles’
    nbrOfFiles.SNPsNormalization: no visible global function definition for
     ‘nbrOfFiles’
    nbrOfFiles.SampleNormalization: no visible global function definition
     for ‘nbrOfFiles’
    process.NSANormalization: no visible global function definition for
     ‘getChipType’
    process.NSANormalization: no visible binding for global variable
     ‘AffymetrixCdfFile’
    process.NSANormalization: no visible global function definition for
     ‘getGenomeInformation’
    process.NSANormalization: no visible global function definition for
     ‘throw’
    process.NSANormalization: no visible global function definition for
     ‘getRam’
    process.NSANormalization: no visible binding for global variable
     ‘aromaSettings’
    process.NSANormalization: no visible global function definition for
     ‘getNames’
    process.NSANormalization: no visible global function definition for
     ‘getPath’
    process.NSANormalization: no visible global function definition for
     ‘getFile’
    process.NSANormalization: no visible global function definition for
     ‘getName’
    process.NSANormalization: no visible global function definition for
     ‘getUnitsOnChromosome’
    process.NSANormalization: no visible global function definition for
     ‘getPositions’
    process.NSANormalization: no visible global function definition for
     ‘str’
    process.SNPsNormalization: no visible global function definition for
     ‘throw’
    process.SNPsNormalization: no visible global function definition for
     ‘getNames’
    process.SNPsNormalization: no visible global function definition for
     ‘getFile’
    process.SNPsNormalization: no visible global function definition for
     ‘findUnitsTodo’
    process.SNPsNormalization: no visible global function definition for
     ‘getRam’
    process.SNPsNormalization: no visible binding for global variable
     ‘aromaSettings’
    process.SNPsNormalization: no visible global function definition for
     ‘str’
    process.SNPsNormalization: no visible global function definition for
     ‘getChipType’
    process.SNPsNormalization: no visible global function definition for
     ‘getPath’
    process.SNPsNormalization: no visible global function definition for
     ‘extractMatrix’
    process.SNPsNormalization: no visible global function definition for
     ‘getName’
    process.SNPsNormalization: no visible global function definition for
     ‘getFullNames’
    process.SampleNormalization: no visible global function definition for
     ‘getChipType’
    process.SampleNormalization: no visible binding for global variable
     ‘AffymetrixCdfFile’
    process.SampleNormalization: no visible global function definition for
     ‘getGenomeInformation’
    process.SampleNormalization: no visible global function definition for
     ‘throw’
    process.SampleNormalization: no visible global function definition for
     ‘getNames’
    process.SampleNormalization: no visible global function definition for
     ‘getRam’
    process.SampleNormalization: no visible binding for global variable
     ‘aromaSettings’
    process.SampleNormalization: no visible global function definition for
     ‘getPath’
    process.SampleNormalization: no visible global function definition for
     ‘getFile’
    process.SampleNormalization: no visible global function definition for
     ‘getName’
    process.SampleNormalization: no visible global function definition for
     ‘str’
    sampleNByTotalAndFracB.numeric: no visible global function definition
     for ‘throw’
    sampleNByTotalAndFracB.numeric: no visible global function definition
     for ‘str’
    setTags.NSANormalization: no visible global function definition for
     ‘trim’
    setTags.SNPsNormalization: no visible global function definition for
     ‘trim’
    setTags.SampleNormalization: no visible global function definition for
     ‘trim’
    snpsNByTotalAndFracB.matrix: no visible global function definition for
     ‘throw’
    snpsNByTotalAndFracB.matrix: no visible global function definition for
     ‘str’
    snpsNByTotalAndFracB.matrix: no visible global function definition for
     ‘rowAlls’
    Undefined global functions or variables:
     AffymetrixCdfFile CNA Object approxfun aromaSettings byPath extend
     extractMatrix findUnitsTodo getAsteriskTags getChipType getFile
     getFullName getFullNames getGenomeInformation getName getNames
     getPath getPathname getPathnames getPositions getRam getRootPath
     getTags getUnitsOnChromosome hist median nbrOfFiles newInstance
     packageDescription rowAlls rowMedians segment setTags str throw trim
     verbose
    Consider adding
     importFrom("graphics", "hist")
     importFrom("stats", "approxfun", "median")
     importFrom("utils", "packageDescription", "str")
    to your NAMESPACE file.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-ix86+x86_64, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.0.32
Check: Rd line widths
Result: NOTE
    Rd file 'NSANormalization.Rd':
     \examples lines wider than 100 characters:
     by <- 50e3; # 50kb bins; you may want to try with other amounts of smoothing xOut <- seq(from=xRange[1], to=xRange[2], by=by);
     plot(getSignals(cnCNPS), getSignals(cnSNPS), xlim=Clim, ylim=Clim); abline(a=0, b=1, col="red", lwd=2);
    
    These lines will be truncated in the PDF manual.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-release-linux-x86_64

Version: 0.0.32
Check: package dependencies
Result: NOTE
    Depends: includes the non-default packages:
     ‘R.methodsS3’ ‘MASS’ ‘matrixStats’ ‘R.oo’ ‘R.utils’ ‘aroma.core’
     ‘aroma.affymetrix’ ‘DNAcopy’
    Adding so many packages to the search path is excessive and importing
    selectively is preferable.
Flavors: r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-release-windows-ix86+x86_64, r-release-osx-x86_64, r-oldrel-windows-ix86+x86_64

Version: 0.0.32
Check: package dependencies
Result: ERROR
    Packages required but not available: ‘aroma.core’ ‘aroma.affymetrix’
    
    Depends: includes the non-default packages:
     ‘R.methodsS3’ ‘MASS’ ‘matrixStats’ ‘R.oo’ ‘R.utils’ ‘aroma.core’
     ‘aroma.affymetrix’ ‘DNAcopy’
    Adding so many packages to the search path is excessive and importing
    selectively is preferable.
    
    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
    manual.
Flavor: r-oldrel-osx-x86_64